NAT2 now released on PharmVar

PharmVar and PharmGKB are excited to share that NAT2 has been transitioned into the PharmVar database and updated accordingly on PharmGKB. NAT2 metabolizes several pharmaceutical substrates, including isoniazid, hydralazine, amifampridine, procainamide and sulfonamides, as well as some highly carcinogenic arylamines. NAT2 enzymatic activity varies considerably between individuals, due to polymorphisms in NAT2 coding sequence that may be found more commonly in some populations than others. NAT2 alleles usually contain more than one single nucleotide variation (SNV), with specific variants defining different allelic groups. Given the complex haplotypic nature of NAT2 alleles, phasing of SNVs to determine diplotype from genotype can be difficult. It is therefore important to maintain up-to-date information regarding sequence variation and star allele (haplotype) definitions to facilitate accurate genetic testing, genotype interpretation and phenotype prediction in the research and clinical settings.

Some drastic changes have been made to NAT2 nomenclature during transition from the original Database of Arylamine N-Acetyltransferases (NATs) to the new “star” allele definitions on PharmVar:

The NAT2 reference allele has now changed: The NG_012246.1 RefSeq differs from X14672.1 (which was used in the past to define star alleles) at the position that corresponds to c.803 (rs1208), where X14672.1 has “A” while NG_012246.1 has “G”. Thus, depending on which reference sequence is utilized, this position is reported as either reference or variant. The transition of allele definitions to the NG_012246.1 RefSeq caused “variant switching”, meaning that all star alleles which were previously described as having c.803A>G lost this variant, as “G” is now considered reference, while all other star alleles gained c.803G>A, as “A” is now considered variant.

The new reference allele is now catalogued as NAT2*1: The sequence of NG_012246.1 RefSeq corresponds to the allele that was formerly described as NAT2*12A. Its renaming as NAT2*1.001 facilitates the application of PharmVar rules to NAT2 allelic nomenclature, while it also enables the use of NAT2*1 name to describe the reference allele, in line with the star allele nomenclature of other pharmacogenes. To avoid confusion during the transition from the legacy to the new nomenclature, *12 is now retired. Having a NAT2*1 allele grouping in place also facilitates NGS analyses using GRCh38 as a reference.

NAT2*4 is no longer considered as the reference allele: Alleles carrying c.803G>A as their only amino acid changing SNV will be called as *4 according to the new nomenclature. This includes the former NAT2*4 reference allele of sequence X14672.1, now considered a variant and listed as NAT2*4.001. Although this will no longer be used as a reference, it is considered to be functionally equivalent to NAT2*1.001 (formerly NAT2*12A) and may still be used to compare the enzymatic or structural properties of polymorphic NAT2 proteins.

Star alleles have been renamed: Several NAT2 star alleles have been renamed to conform to PharmVar rules during the transition from the legacy nomenclature to the PharmVar database.

Not all previously defined star alleles have been transferred: In the past, it has not always been clear how a NAT2 haplotype was determined. Many have been inferred via computational phase analysis and were not verified experimentally. In the case of haplotypes where the available evidence from the literature was deemed insufficient to support confident allele definition, those haplotypes were not transferred to PharmVar, but they will remain posted on the original Database of Arylamine N-Acetyltransferases (NATs).

PharmGKB-annotated NAT2 alleles that are not transitioned into PharmVar will remain on PharmGKB with the original Database of Arylamine N-Acetyltransferases (NATs) name (e.g., NAT2*6J). PharmVar-transitioned NAT2 alleles are indicated on PharmGKB NAT2 allele pages with the new "PharmVar Allele" tag (e.g., NAT2*4).

The requirements for new allele definition have changed: In the past, reporting only the SNVs in the NAT2 coding region was sufficient to define new star alleles. According to PharmVar rules, new NAT2 alleles must cover SNVs within defined coordinates that enclose the 5’ untranslated region (including the untranslated first exon), the coding exon, the exon/intron junctions, and the entire 3’ untranslated region relative to genomic reference sequence NG_012246.1. Former alleles covering only the coding region have been annotated with a limited evidence level, as they may have additional variants that were not captured when the allele was first defined.

During the course of updating NAT2 nomenclature, we have been able to confirm several of the former haplotypes, while also identifying new ones. PharmVar encourages submissions of novel haplotypes for star allele definition, as well as for existing definitions to either raise their evidence levels from Limited or Moderate to Definitive, or to solidify their status of Definitive.

Additional information has been summarized in the Read Me and Change Log documents available on the PharmVar NAT2 page. Also please consult the “NAT2 Look-up” table available under “More Documents” on the same page for an up-to-date record of alleles transferred and a quick reference of PharmVar and legacy star allele names.

We would like to thank all members of the PharmVar NAT2 Gene Expert Panel for their massive contribution to this project, as well as the NAT Gene Nomenclature Committee for their services to the NAT community since 1998.

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